The shopping cart (under product settings > options tab) lets you set main option and then a dependent sub-option. This isn't enough with more complex products. I would suggest more flexibility in terms of the number of sub-option levels in the hierarchy. Perhaps at least a thrid level down. 

I would also suggest that you can attach price differences at the sub-option levels.

A practical example would be options packages on cars, where you can only order something if you already selected previous options. Perhaps only the car with dual tone paint has two special interior packages available, and you must choose one. Then within each interior package there are further options (unique to each package - so they are dependent on the previous selections in the hierarchy).

Would also suggest a setting specifying if some might be mutually exclusive (single choice only) and other multiple selections allowed.